What is “Open Notebook Science”?

The term “open notebook science” was first coined by Jean-Claude Bradley in a blog post^[1] to clarify and distinguish between several related concepts in the open access movement in science. Bradley defines the term to mean that

there is a URL to a laboratory notebook… that is freely available and indexed on common search engines. It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world. Basically, no insider information.

Open notebook science is thus analogous to open source software, but applies to all types of data and not just source code. It is also distinct from but related to open access publication, which denotes the public availability of preprints of journal articles. Bradley coined the term in order to properly describe the philosophy behind the UsefulChem^[2] project.

The principle behind open notebook science is that anyone can access the primary research record of a project, including preliminary results of experiments, and even raw data as it is gathered. By this definition, open source software projects in computer science, such as those found on SourceForge^[3], are also open notebook science projects if the “notebooks” are taken to mean not just the source code but also the web pages, documentation, forums, and other materials associated with these projects.

For the purposes of open notebook science, a “notebook” is thus quite broadly defined: it might be anything from scribbles which appear to be random gibberish to outsiders to somewhat polished half-baked thoughts. However, it should be noted that traditional notebooks are probably similarly broad in their diversity.

For computer science theorists, an open notebook might consist of a research diary where one records one’s thoughts on open problems and questions which one is working on.

I believe that computer scientists should lead the charge to adopt open notebook science, and in this essay I will explain why I hold this belief.

Examples of Open Notebook Science Projects

Perhaps the best way to illustrate the concept of open notebook science is by way of example. Many of the large and well-known open notebook science projects are in chemistry (cheminformatics) and biology (bioinformatics), disciplines in which it is typical to generate and work with large amounts of data. This data may be costly to produce in terms of money and/or time, and there may be a great deal of redundancy and reduplication between the efforts of different laboratories or research groups. Two examples of large open notebook science projects are OpenWetWare^[4] and UsefulChem^[5].

The goals of the OpenWetWare project are to “support open sharing of research, education, publication, and discussion in biological sciences and engineering”, according to their mission statement^[6]. To this end, their web site provides blogs and wikis to users and research groups. The wikis are specialised for certain tasks, such as lab notebooks and hosted courses.

The UsefulChem project is an open notebook science project in chemistry originated by the Bradley Laboratory at Drexel University. It is hosted on Wikispaces, a web site that allows users to set up free wikis, and has an associated blog^[7] hosted on Blogger.com, another free service. The UsefulChem project illustrates how researchers in fields outside of computer science are using readily available tools to create their open notebook science projects.

I was unable to locate any open notebook science projects of a similar focus and scope for physics and computer science. As note above, projects to develop open source software, hosted on publicly accessible code repositories such as SourceForge^[8] or Google Code^[9], might be considered examples of open notebook science projects if all documentation and other materials related to the projects are also accessible to the public. And the physics community is actually an early adopter of open access publishing, with its embrace of the arXiv^[10] repository of electronic preprints (or e-prints) in 1991.

The quantum computing community in particular has two wikis, Quantiki^[11] and Qwiki^[12]. However, these wikis are intended to be references for researchers rather than notebooks for recording ongoing research.

Many individual researchers keep openly accessible notebooks, or have blogs on which they discuss their research semi-regularly. These are far too numerous to list, but there are a number of portals such as BlogScholar^[13] in which research-related blogs are organised by category.

For researchers outside of computer science, technologies such as blogs and wikis are only tools to assist in their research. For computer scientists, however, these technologies and their impact on society are in and of themselves objects of study. It is therefore a little disappointing that open notebook science is not more widely practised in the computer science community.

Advantages of Open Notebook Science

The movement towards openness in science is based on the belief that sharing and cooperation leads to swifter progress than hoarding and competition.

Even leaving aside for the moment the advantages of openness, there are many benefits to using the latest note and record keeping technologies, such as wikis and blogs, whether or not they are made public. These include advantages common to all derivatives of digital text formats, such as the legibility of typed text as opposed to handwriting, the ability to copy, share, search, and archive notes, and the portability and extensibility of the notes unconstrained by the limitations of physical notebooks (or loose sheets of paper), which may be difficult to carry around and may be misplaced.

Technologies such as blogs and wikis also perform the role of versioning software, keeping a timestamped history of all edits, arbitrating between conflicting ones, and maintaining a record of all contributions and their contributors. Furthermore, these technologies also offer advanced search and organisational capabilities, such as the labeling of notes with tags, the arrangement of notes into a hierarchy of categories, and the inclusion of semantics through metadata. These search and record keeping capabilities would be very useful to scientists when the time comes to write grants and progress reports.

The use of digital media also means that notes may be dynamic and interactive. For example, instead of writing a mathematical formula, a digital notebook might contain a form for evaluating that formula with different inputs. A more trivial example of interactivity is that digital notebooks allow the reader to go back and forth between the main body of a text and a footnote^[14], or between different pages or even different documents, very quickly, by clicking with a mouse or using keyboard shortcuts instead of fumbling with physical sheets of paper.

Making a notebook public brings several benefits in addition to the above. The sharing of notes is made much easier if one can simply pass around a URL (or DOI) instead of copies. An open notebook is available “everywhere” (limited by Internet access, which is ubiquitous at all research institutions anyway), and the notebook cannot be misplaced.

Many of the advantages of open source software also apply, mutatis mutandis, to open notebook science as well. An open notebook potentially has “many eyeballs” on it, allowing researchers other than the main investigators to submit “patches”, i.e., contribute slight tweaks or even major suggestions. This facilitates scientific discovery and creates more opportunities for better scientific conversations.

Considering the large number of open scientific problems and the diverse backgrounds of scientists, there are bound to be many instances in which the solutions to problems are known to or can be easily produced by researchers other than those who are actively examining them. Conversely, there may be discoveries which do not appear important in one field but which can bring about significant progress in another. Open notebooks allow minor questions or serendipitous discoveries to be made publicly known without having to attach them to a paper primarily about another more major (and possibly not very related) result. This is, in fact, what is already happening in several blogs maintained by scientists^[15].

The open availability of “insider information” such as data, ideas, and detailed experimental procedures or proofs of theorems which have been condensed in published journal papers for brevity, allow these to be verified and increases the accountability of scientists and the transparency of science.

By performing their work in the open, it becomes possible for scientists to more efficiently allocate their resources, contributing their expertise where it is needed and summoning the expertise of others when that is required. The scientific community as a whole benefits from this openness. Keeping an open notebook also helps the individual scientist, because it increases his or her visibility in the major search engines.

There are benefits to the general public as well. The public accessibility of notebooks which are research diaries serves as a kind of real-time science journalism. This gives the public a closer look at the actual lives of scientists (which one hopes would dispel negative stereotypes), and helps to acquaint new researchers with what the life of scientists are actually like. The low cost of entry of starting a blog or a wiki might also serve to get young scientists, such as ambitious high school students, involved in the research process early.

Credit, Plagiarism, and Other Issues

The concept of open notebook science is not without its problems. The primary concern seems to be the issue of priority, or, in the common parlance, “getting scooped”.

Science has changed considerably since the days when scientists such as Galileo Galilei or Robert Hooke would encrypt their findings as Latin anagrams to establish their claim while concealing the actual contents of their discovery to give them a head start on research over their rivals. The history of science is filled with rancorous debates over who first came up with certain ideas, or whether an idea should be attributed to an originator who subsequently did very little with it or to someone who later developed and expanded on it.

Given the principle of “no insider information”, a scientist might be understandably concerned about intellectual property theft. There are, essentially, two ways to address the issue: social and legal.

As some commentators^[16] have observed, there are already social norms in place which heavily discourage plagiarism and lack of proper attribution by scientists and scholars. This may be called the “French chef” approach to protecting intellectual property, after a study by Fauchart and von Hippel^[17] who showed that the contents of recipes among accomplished French chefs are protected by a system of implicit social norms, rather than by law. Such a “norms-based” intellectual property system may deter would-be plagiarists and people who do not give proper credit. More public information about when each scientist came up with or worked on a particular idea should in theory decrease disputes about priority rather than increase them. When scientific conversations are timestamped, viewable to the public, and indexed and cached by multiple search engines and crawlers, it would be extraordinarily difficult to have honest disputes over the history of events related to a claim of priority. Social norms among scientists should encourage offers of collaboration and discourage “scooping”.

When norms-based deterrents against intellectual property theft are insufficient, there is always recourse to law-based systems. Creative Commons^[18], for example, provides a number of legal tools for sharing intellectual property, including various free licenses with different stipulations^[19] which may be attached to creative works.

An open notebook science web site or project may choose a license based on its specific needs and legal requirements. Most open notebook science web sites have licenses that allow sharing and distribution conditioned only on attribution. Others add a “share alike” clause, which allows derivative works conditioned on these being under the same, similar, or compatible license. There are also licenses which forbid derivative works, commercial usage, or both.

Some proposed solutions to the problem of intellectual property theft with open notebooks are technical rather than social or legal in nature, such as restricting information to registered users or introducing a delay in the notebook. However, such solutions violate the spirit of “no insider information”, and the result could not be properly called open notebook science.

There are several other intellectual property issues related to open notebook science, such as what constitutes prior publication for peer-reviewed journals, and premature disclosure for the purposes of obtaining patents. Many journals, however, already accept papers which have previously appeared as preprints in repositories such as the arXiv^[20]. However, patent law has yet to catch up to many recent developments in technology.

The release of large amounts of data which have not undergone careful review raises a number of problems in trust and credibility. If a set of data is posted publicly before it is thoroughly checked, it may contain errors which may be propagated. However, as the open source movement shows, for active projects, bugs are usually caught and fixed quickly. Furthermore, it is not clear that reviewers of published papers necessarily check the data used to support the arguments of the papers they review very thoroughly (although, in principle, they should).

The use of data from open notebooks, then, imposes a duty upon the user to be vigilant and to take on some aspects of the role of reviewer. This, however, should be the case anyway, even with peer-reviewed published data. The recent Merck/Elsevier fake journals scandal^[21] amply illustrates the point that even an established publisher of scientific journals should not be naïvely trusted.

Other criticisms of open notebook science deal with the user experience, whether from the point of view of a producer or a consumer of open notebooks. On the one hand, a scientist’s notekeeping style may consist of what may appear to others to be random scribbles, and keeping an open notebook would force him to clean up his spontaneous output and restrain his creativity. On the other hand, most of a scientist’s notes may not be very meaningful to others. But not all open notebooks are meant to be read as research diaries. Rather, search and organisational tools should allow relevant information to be found even in a sea of irrelevancies.

Finally, another criticism of open notebooks is their stability, or the ability to reference their data. But this is a problem that is not unique to open notebooks, and applies to all electronically published information. Solutions include stable URLs or DOIs, or the use of an archival service such as WebCite^[22].

Proposed Process

I believe that computer scientists should adopt open notebook science not only for the benefits discussed above, but because it is a subject that is inherently a part of computer science. Computer scientists, as computer scientists, have a duty to explore technologies for archiving and communicating information as well as their social and legal implications.

I can’t very well advocate computer scientists to make their notebooks publicly accessible without doing so myself. This is why I created the ★grads.net web site (read as “star grads dot net”), as a platform in which to experiment with various aspects of open notebook science.

Currently, the web site consists of four software packages:

• MediaWiki for taking notes and writing papers,
• WordPress for keeping a research diary,
• bbPress for collaborative discussions, and
• Wikindx for bibliography management.

The software packages are integrated with one another, to the extent that this is possible to my knowledge at the moment. For example, it is possible to generate citations using the bibliography management system in both the wikis and the blogs. Furthermore, through the use of the jsMath package, it is possible to typeset mathematical equations using the widely known TeX syntax throughout the web site.

The intention is to use the blog to keep a diary of research activities, such as meetings or talks that I attend, or ideas that I have. These ideas may then be discussed in the blog comments, or if there is serious interest, in the forums. When an idea gets developed enough, a wiki page will be started for it. Some of these wiki pages may then evolve into papers, such as the one you are currently reading. Since this is an experiment, the roles of these tools may change over time.

One of the goals of the web site is to experiment with collaborative paper-writing. Currently, papers are written by passing around the document source through e-mail along with an indication of who is in possession of a virtual “token”. When a paper is sufficiently mature, a draft may be passed around to other researchers for comments. There is in principle no reason why the draft should not be publicly available at every stage for outside comments or suggestions. Wikipedia^[23] has shown that this sort of collaborative process can result in documents of reasonably good quality.

As the history^[24] of this paper shows, it began with a list of headings for the sections that I planned to write. The sections were then filled with rough notes, which were subsequently expanded into this paper.

Papers written in this fashion have not passed peer review, and thus should be treated like preprints on the arXiv or blog posts. Ideally, however, if enough experts participate in the commenting process, such a paper should have been reviewed quite thoroughly. This distributed evaluation process may be called “soft” peer review, as opposed to the traditional “hard” peer review.

At the moment, I am the only user on this web site capable of editing wiki pages, and hence of authoring papers. But the idea is that multiple authors can work on a paper, and contributors may be elevated to the status of co-author if they make significant contributions.

The contents of the ★grads.net wiki are under a Creative Commons Attribution-Noncommercial-No Derivative Works license. The “No Derivative Works” clause may seem a little restrictive, but as the license notes, any of its conditions “can be waived if you get permission from the copyright holder”. The purpose of this clause is to protect the contents of paper drafts until they are finished. Drafts should have the same social protection and status as if they had been written using more traditional means, that is, they should not be cited or used without the authors’ explicit permission.

(I will write out a more comprehensive copyright policy for each section of the web site when I get around to it.)

This paper is still a draft^[25], and I invite your comments and suggestions, which I will take into consideration in revising it. There is an acknowledgements section at the end of this paper for listing contributors. The goal is to submit this paper somewhere for “official” publication after it is sufficiently polished^[26].

For Further Reading

The Wikipedia article on Open Notebook Science actually isn’t bad and discusses many of the same points.

Acknowledgements

The author would like to thank Mina Razaghpour for her suggestions.

Bibliography

Related posts:

1. Open notebook science
2. An essay on open notebook science
3. Overcoming my writer’s block, part 5: writing about open notebook science in high school

Because I’m using Jarnal to annotate these papers, I wanted to integrate the ability to launch Jarnal into Wikindx itself, and also to store the annotations in Wikindx along with the attached documents.

I wrote the Annotate With Jarnal plug-in module for Wikindx initially for my private use, so it’s not very polished. But it gets the job done.

The module adds an “Annotate With Jarnal” menu item to the “Resources” menu in Wikindx. To use it, copy the URL of an attached PDF file, and paste it into the module’s input box. The module then generates a Jarnal Meta File which (if everything is set up correctly) launches Jarnal with the PDF file as the background.

Here is a series of screen shots showing the module in action:

The result of the above sequence of steps is that Jarnal fetches the PDF file from Wikindx, and displays it for annotation:

The annotations can be saved using Jarnal’s “Network Save” feature. This writes the Jarnal file back to the “attachments” subdirectory in the Wikindx directory on the web server, with a file name created from appending the “.jaj” extension to the hash code of the annotated file. The next time the PDF file is opened through the module, the annotations will be loaded along with the PDF file.

A user must be logged in to Wikindx to use the module. However, beyond that, there is currently not a lot of security. Furthermore, the interface is not very easy to use. Ideally, there would be an “annotate” button or link next to each attached PDF file, so that the user does not have to bother with copying the URL and pasting it. Right now, there’s nothing to stop the user from entering a malformed or nonsense URL, but in most cases the module will respond by displaying an error message or doing nothing.

The module can also be used with the Macro Expander plug-in for WordPress, to provide a link to directly annotate a PDF file from a WordPress blog entry. I kept my research notes in a private WordPress blog on my laptop, and this feature allowed me to link to and annotate the relevant papers directly from my research notes.

For more information, and the source files, see the module’s web site on launchpad.net.

– davinci 11779

Related posts:

1. Wikindx macro plug-in for WordPress
2. Converting DigiMemo files to Jarnal format
3. Using the Ajaxified Expand Post Now plug-in with Rob Miller’s Footnotes plug-in

The answer is “yes”.

It took me a while to figure this out, and in retrospect the answer is (maybe) obvious.

I think this question is a very nice example of a research question for a beginning Ph.D. student, in that it’s not too difficult, and at the same time could potentially lead to a body of research culminating in a Ph.D. (Although this didn’t happen for me.)

I had been meaning to put my research notes online for a while, but had put it off because they’re not as useful to as many people as they could be, in the form that they’re in.

(I had actually wanted to put all of my research notes online from the very beginning, but refrained from doing so because I didn’t want my parents to find out that I was studying quantum computing, since they had threatened to disown me if I did so. But now that they have disowned me, I no longer have a reason not to write about quantum computing in public.)

In this next series of posts (which might be interspersed between posts about other things), I’m going to write about the experiences I went through, and the topics that I learned, while trying to answer the above question. I’m also going to clean up the relevant sections of my research notes, and post them online, along the way. I hope that my posts and research notes will be useful not only to other quantum computing researchers, but also to potential graduate students in any theoretical field who might have to undergo similar experiences when they begin their research.

I’ve created a page on my wiki where my notes on this research question will eventually go.

Interestingly, I’ll be inadvertently implementing the Quantum Pontiff’s idea of a delayed open notebook, since the research I’ll be writing about took place about three years ago.

– davinci 11744

No related posts.

I have tried to keep the essay as impersonal as possible. The benefits given in the essay of keeping an open notebook apply to any scientist, but I especially have some very personal reasons, if not for advocating the practice, then at least for engaging in it myself. After all, the entire project of building this web site started out as an effort to overcome my writer’s block in writing my Ph.D. Research Proposal.

In a way, I’m making up for what I think I should have been doing since the beginning of graduate school, and maybe even earlier. I’ve been thinking about the effects of communications technologies on science and society since high school. But because my parents criticised me every time they found my name online, I was forced to keep my online presence to a minimum. Many of the things that I foresaw have come true or are coming true — but ironically without my participation, until now.

I’ve written about how I was unable to participate in collaborative paper-writing in a previous post, and also about how turning my attention to another topic was my defense mechanism whenever I became stuck and could not make progress on something. The more I thought about my inability to work, the more compelled I felt to think about how I would be working if I had absolutely no concerns about being criticised and was completely free to disregard the way things are currently done.

I was an extremely prolific writer in high school, in large part due to having had a lot of friends at the time with a large variety of interests. I would pass around my writings and get comments, which would inspire further revisions and motivate me to write even more. To become productive again, I need to replicate this kind of environment.

The number and variety of the people I regularly associate with nowadays have narrowed considerably since that time, partly as a result of having moved around for graduate school, and partly due to the nature of graduate school itself (especially the departmental segregation inherent to universities), but primarily because of my parents’ continual attacks against anyone I might associate with. The natural antidote to the waning of my social circle would have been to expand it through meeting people from other departments of the university, or by using online social networking tools, but I had for the most part done neither since starting graduate school. When I start interacting with more people again, I will try to build up my academic social circle through this web site.

For me, the archival features of blogs and wikis are much more important than the mere ability to keep a timestamped record of my work. I have a habit of destroying my own work due to the pain caused by my parents’ continual criticisms, and this technology makes it much more difficult to actually act on my self-destructive urges. I regret that I have lost a lot of my work in this way.

In the essay, I wrote about the fear that many people seem to have of getting “scooped”. I want to elaborate on this, but my perspective probably does not apply to most other people. First, I had the opportunity to be a part of the field of quantum computing early on when many of its important discoveries were made, but my parents had deprived me of this by forbidding me to continue my studies at the time. Subsequently, I have returned to the field, but without the background typical of most researchers. I’m therefore somewhat indifferent to being “scooped”, because it couldn’t possibly be worse than what my parents had already done to me.

Second, my experience has been that most of the time, I am stuck on some minor obstacle that (I imagine) someone with a more suitable background could easily overcome. The only problem is that I often don’t know who that someone is. Or, even if I had some people in mind whom I thought could clarify things for me, I may feel that my questions are too minor to bring to their attention or that it would be impolite to spam them (i.e., send them unsolicited e-mails).

It would have helped my progress considerably if I had a forum where I could freely discuss things that I don’t quite understand, with peers who are in a similar predicament but who have different backgrounds and training. Experts could then volunteer their insights without anyone feeling that they were imposing upon them. I suppose that such fora already exist in the form of newsgroups and so on, but that I simply haven’t made use of the resources actually available to me due to my self-imposed minimal presence online. But newsgroups are generally far too broad in scope. I think every computer science department should have an internal bulletin board system.

In any case, I would be glad to be “scooped” most of the time, if it meant that my time was freed to make progress where it was important instead of “re-inventing the wheel”. I suspect that this might be true of other researchers to various degrees.

I wrote in the essay that the low cost of starting a blog or wiki might motivate ambitious young people to get involved in science at an early age. When I was in high school, I was always looking for scientific data to play around with. I also used to enjoy reading the notebooks of historical scientists. Access to the notebooks of contemporary scientists is something that I definitely would have wished to have. Open notebooks could very well shape the careers of the next generation of scientists.

– davinci

Related posts:

1. Overcoming my writer’s block, part 5: writing about open notebook science in high school
2. Open notebook science
3. Why Computer Scientists Should Adopt Open Notebook Science

I am a member of the first generation in which the masses have easy access to the tools for creating mass media. When you think about it, it’s incredible how much has changed even in just one decade. At that time, if you wanted to disseminate your message on a shoestring budget, you’d type or print your pamphlet, bring it to the printshop or photocopier, make however many copies, and physically distribute them. (And if your audience was really illiterate, you’d speak into a cassette recorder and give out copies of the tape.) People with kooky or dangerous ideas were thus limited in the reach of their message or the amount of damage they could do.

But with the advent of the mass popularisation of the Internet, the dynamics have suddenly changed. Now anyone can easily broadcast any message whatsoever and have the potential to reach the entire world. In high school, I became very interested in the social consequences of cheap mass media technologies with global reach. Some of the effects of these technologies on individuals and on society were being discussed in some popular publications of the time, but I really felt that the importance of the subject was generally drastically underestimated even by the people who were paying attention. I was interested in the civilisational consequences of these technologies, and no one that I knew of had written anything about that — so I set out to fill the gap.

Many of the things that I had thought and written about have come to past, such as social networking sites and collaborative encyclopedias. I do not claim by any means to be prophetic in this: these ideas were discussed, and some implementations even attempted, long before the technology or the critical mass of participants existed to finally make them successful. Some of my influences at this time were Wired magazine, which had started publishing shortly after I began high school, and the writings of Marshall McLuhan and Harold Innis.

Incidentally, both of these writers were Canadian — as were the people who had recommended them to me, when I asked around for suggestions on reading materials related to the role of communications in civilisation. I wonder, if I had asked a bunch of Americans (or Europeans, or Asians, or whatever), would I have been pointed to a different set of thinkers? The medium might have tainted the message in this case; but if it had, I think it was ultimately to my benefit.

I was particularly interested in how these new communications technologies would be put to use by what might be considered two “extremes”, in some sense, of the current global civilisation. At one extreme, I wondered how the Internet was going to affect the way science was carried out and communicated. At the other extreme, I thought about how the new media might become the vehicles of irrationality and superstition, carriers of the very cultures which would have rendered the creation of these media impossible in the first place — a topic to which I will devote the next post. Here, I will write briefly about my thoughts in high school on what is now called “open notebook science”.

Once upon a time, science was the privilege of the elite; scientists routinely kept their discoveries secret except to a close circle of colleagues, or delayed publication for as long as possible. The system of scientific journals, made possible by the invention and subsequent spread of the printing press, changed this by giving scientists an incentive to share their results: credit for their discoveries in the historical record. The existence of a platform for scientific publication in turn allowed amateurs to contribute their discoveries.

The rapid advances in scientific understanding and the accumulation of scientific knowledge, made possible in part by the system of scientific journals, has since created a situation in which it seems that amateurs could no longer make pivotal contributions to science the way some have done so even a century earlier. Science has become specialised to a degree that significant training was needed even to begin research in many fields; and in addition, amateurs lacked access to the voluminous data and expensive equipment available to universities and research institutes.

When I was thinking about this, I was actually involved in a project at the University of Toronto to study variable stars, under the direction of Dr. John Percy. It involved a very primitive form of distributed computing: every two weeks or so, I would visit the university and receive some data on floppy disks (or several megabytes of data, if you’re too young to know what floppy disks are). I would take that data home, analyse it on my home computer, and on my next visit I would return the results and receive a new batch of data. The results of my analysis would be merged with those of others and processed further.

I had the sneaking suspicion that my contributions were not strictly speaking necessary, and that the entire setup was a charade the primary motivation of which was to involve high school students in the scientific research process. (Surely the university had the resources to process data at a rate much faster than several megabytes every two weeks, even if the project had the absolute lowest priority out of all the projects in the entire university!) But I enjoyed visiting the university too much to bring this up.

In any case, I thought a lot about distributed and cooperative computing at the time. Presumably, Dr. Percy had obtained the data from somewhere electronically; I didn’t think he had a stack of floppy disks delivered to him every two weeks! I don’t recall if the raw data was available to the public or not — my faint recollection is that I had to sign something or other before I was granted access to it — but I didn’t see why in principle it couldn’t have been. After all, I was just a high school student with a computer. There was no particular reason why anyone with a computer and an Internet connection — whether amateur or professional — could not have just downloaded the data themselves and experimented with it, perhaps in collaboration (or even in competition) with others. Furthermore, there was no reason why they couldn’t have blogged about their experiments while they were performing them, or received live feedback from other researchers while doing so — rather than (or in addition to, if they wished) writing a scientific paper selectively after the fact.

(It’s true that the word “blog” didn’t actually exist at the time — but the activity most certainly did. It was just called “writing on a semi-regular basis and sharing your writings with other people”. I concede that it doesn’t roll off the tongue quite as nicely, but I used to engage in this activity all the time. Since it’s such a convenient word, I’m going to use it when I feel it’s appropriate — even if it means being anachronistic.)

A large part of the problem with making advances in modern science is its scope — science is so large, and there are so many subfields, that scientists in one field are often unaware of results or techniques from other fields which might be applied to solving problems in their own. I thought that information sharing and retrieval technologies would provide a great deal of aid in overcoming this problem. Scientists could, on the one hand, write openly about problems which they were working on or which they had solved; and on the other hand, they could search through the blog archives of other scientists to see if anyone else had worked or were working on similar problems.

So I had this vision of the future of science which hasn’t quite come true yet. But I’ve written too much about it already — I’m supposed to be writing about the causes of my writer’s block! (Of course, the fact that I’m writing again is a very good thing, no matter what I’m writing about.) I will have more to write about this “open notebook science” business later, since I intend it to be one of the main topics of this blog.

– davinci

Related posts:

1. Overcoming my writer’s block, part 3: science writing in high school
2. Overcoming my writer’s block, part 4: high school and being editor-in-chief
3. Overcoming my writer’s block, part 2: elementary school, ESL, and fiction

To begin with, I didn’t find any ready-made projects which exactly suited my needs. The most impressive, and the one which came the closest to what I was looking for, is OpenWetWare, but its focus is on biology and biological engineering. Chemists have also gotten into the act with UsefulChem, which is hosted on wikispaces.

I did not locate any project of a similar scope or scale for physics or, perhaps ironically, computer science. The physics community is actually an early adopter of electronic scientific publishing, with its embrace of the arXiv since 1991. And the quantum community has not just one but two — count ‘em, two — whole wikis to itself: Quantiki and Qwiki. Michael Nielsen (the Mike of Mike and Ike, which is widely considered the standard text for quantum computation) has written an extensive post about the opening up of scientific culture.

Another reason for building the site myself, instead of relying on a ready-made solution, is the degree of control I would have over its customization. For a biologist or chemist, communications technologies such as blogs and wikis are only tools. But for a computer scientist, these technologies are themselves objects of study.

Following OpenWetWare’s example, I have installed MediaWiki (for wikis) and WordPress (for blogs), and I have also added bbPress (for bulletin boards) and WIKINDX (for bibliography management) into the mix.

Despite the fact that the name ★grads.net, which came to me in a fit of inspiration, suggests multiple grad(uate student)s, for now this experiment in open notebook science is mine alone.

– davinci

No related posts.

This blog and this website are my contributions to the open notebook science movement. I strongly believe that modern communication technologies will dramatically change (and in fact have already been dramatically changing) the way science is done and disseminated. Many more people have access to scientific information than ever before, and at the same time, science policy at the highest levels of government have the potential to affect the lives of everyone in the world. Science is no longer the enterprise of an elite few, but the common heritage and responsibility of every person on the planet — and we can no longer afford for it not to be open.

– davinci

Related posts:

1. An essay on open notebook science
2. Overcoming my writer’s block, part 5: writing about open notebook science in high school
3. Why Computer Scientists Should Adopt Open Notebook Science